The mechanism by which DNA intercalating agents produce protein-associated DNA strand breaks in mammalian cells and the significance of these effects were studied. Various cell and subcellular targets were examined for their ability to demonstrate this reversible DNA effect. It appears to differ from other forms of DNA scission in its inability to stimulate cellular responses commonly elicited by DNA breaking agents, its dissociation from drug-induced cytotoxicity, its equivalent production in repair-proficient and repair-deficient human cells, and its enhanced production in the DNA from cells with actively transcribing chromatin, or with hypomethylated DNA. Aspects of the cytotoxicity, transport and DNA breaking potency of m-AMSA suggested a clinical trial testing its utility as a continuous infusion. This trial has been completed.